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TPR MCAT Biochemistry > Amino Acids and Proteins > Flashcards

Amino Acids and Proteins Flashcards

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MCAT flashcards
1
Q

What is meant by all amino acids are amphoteric?

A

They have the ability to act as acids and bases in reactions.

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2
Q

pKa of carboxyl and amino groups

A

carboxyl = 2

amino groups = 10

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3
Q

When the pH of the solution is less than the pKa of an acidic group, the acidic group will be mostly__

A

When the pH of the solution is less than the pKa of an acidic group, the acidic group will be mostly in its protonated form

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4
Q

When the pH of the solution is greater than the pKa of an acidic group, the acidic group will be mostly____

A

When the pH of the solution is greater than the pKa of an acidic group, the acidic group will be mostly in its deprotonated form

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5
Q

henderson hasselbalch equation

A
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6
Q

calculating pI of a molcule (i.e. AA) with 2 functional groups

A

average the pKa’s of the two functional groups

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7
Q

How to compare the pH of a solution to the pKa of the functional group of an AA and determine if a site is mostly protonated or deprotonated?

A

If the pH is higher than the pKa, the site is mostly deprotonated; if the pH is lower than the pKa, the site is mostly protonated

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8
Q

How are polypeptides linked together

A

Peptide bond - b/w the carboxyl group of one AA and the α-amino group of the another AA

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9
Q

polypeptide backbone formation

A

N-C-C-N-C-C

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10
Q

How do we break apart proteins?

A

Via Hydrolysis, by another protein called a proteolysis or proteolytic cleavage and the enzyme is called a protease

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11
Q

Primary protein structure

A

AA sequence

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12
Q

Secondary structure

A

H-bonding between the backbone groups (NH and CO)

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13
Q

Tertiary Structure

A

folding due to side chain interactions within a polypeptide

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14
Q

types of interactions in Tertiary Structure

A

Noncovalent

  1. acid/base (electrostatic)
  2. polar/polar
  3. nonpolar/nonpolar

Covalent

  1. disulfide bridges (b/w cysteine)
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15
Q

Quaternary Structure

A

side-chain inreractions between different polypeptides.

NOT all proteins have this structure

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16
Q

How do we drive endergonic reactions forward?

A

couple it with exergonic reactions

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17
Q

Hydrolase

A

hydrolyzes chemical bonds (including ATPases, proteases, and others)

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18
Q

Isomerase

A

rearranges bonds within a molcule to form an isomer (i.e. second half of PPP)

19
Q

Ligase

A

forms a chemical bond (e.g., DNA ligase)

20
Q

Lyase

A

breaks chemical bonds by means other than oxidation or hydrolysis (e.g., pyruvate decarboxylase)

21
Q

Kinase

A

transfers a phosphate group to a molcule from a high energy carrier, such as ATP (e.g., phosphofructokinase [PFK])

22
Q

Oxioreductase (give examples as well)

A

runs redox reactions (includes oxidaes, reductases, dehydrogenases, and others)

23
Q

Polymerase

A

polymerization (e.g. addition of nucleotides to the leading strong of DNA by DNA polymerase III)

24
Q

Phosphatase

A

removes a phosphate group from a molecule

25
Q

Phosphorylase

A

transphers a phosphate group to a molecule from inorganic phosphate (e.g., glycogen phosphorylase)

26
Q

Protease

A

hydrolizes peptide bonds (e.g., trypsin, chymotrypsin, pepsin, etc.)

27
Q

Cofactors

A

metal ions or small molecules (not themselves a protein) that are required for activity in many enzymes. Vitamins in our diet serve as precursors for cofactors

28
Q

coenzymes

A

when a cofactor is an organic molecule

29
Q

What is Km?

A

Km is the concentration of substrate [S] required to reach 1/2 Vmax

30
Q

explain affinity and Km

A

It is like an affinity the enzyme has for the substrate and has an inverse relationship.

Increase affinity = decreased Km (less substrate needed to reach Km)

31
Q

What is meant by Vmax what does it depend on?

A

Vmax is the maximum rate of product formation, when the enzymes are completely saturated by substrate

  • Depends on:*
  • enzymes you have
  • enzyme concentration
  • NOT impacted by substrate
32
Q

Competitive Inhibition

A
  • binds at: active site
  • effect on Vmax: No effect (can be overcome by addition of more substrate)
  • e_ffect on Km_: Increased (meaning decreased affinity since there are others competing now)
33
Q

Non-Competitive Inhibitors

A
  • binds at: allosteric site (turn enzymes off)
  • effect on Vmax: decreases (some enzymes are turned off thus less product formation)
  • effect on Km: Unchanged (binds at allosteric site, thus doesn’t affect substrate binding)
34
Q

Un-competitive Inhibitors

A
  • binds at: allosteric site of ES compelx (after substrate binds)
  • e_ffect on Vmax:_ decreases (some enzymes inactivated, less product formed)
  • effect on Km: decreases (greater affinity since the substrate gets locked in)
35
Q

Mixed Inhibitors

A
  • binds at: allosteric site of ES compelx (after substrate binds) OR allosteric site on E alone (Δ shape of active site)
  • effect on Vmax: decreases (since mimic uncom or noncom)
  • effect on Km: increased, decreased, or unchanged (need to know more about inhibitor)
36
Q

Describe Key components of Lineweaver-Burk Plots

A

Inverse Plots: 1/V vs. 1/[S]
V = rate of product formation
[S] = concentration of substrate

y-intercept: 1/Vmax
x-intercept: -1/Km

As you approach interssection point on the graph, the denominator is getting bigger

37
Q

Type of Inhibitors in these graphs:

A
38
Q

Monomers of Carbohydrates and formula

A

Carbohydrates CnH2nOn

39
Q

common monosaccharides

A

6 Carbon Sugars
glucose
fructose
galactose

5 Carbon Sugars
ribose
deoxyribose

40
Q

Most common disaccharides and their constituent components

A

For the MCAT, they will all be something plus glucose

1) Maltose - glucose + glucose
2) Sucrose - glucose + fructose
3) Lactose = glucose + galactose

41
Q

3 most common and their function

A

Glycogen: animal glucose storage
Starch: plant glucose storage
Cellulose: plant structure (humans can’t digest)

42
Q

Functions of Carbohydrates

A
  • Energy
    • cells preferred energy storage
    • think reduction of glucose via cellular respiration
  • Cell surface markers
    • distinguishes b/w different types of cells (liver vs. muscle)
  • adhesion
    • carbs are sticky
43
Q

Monomers of lipids

A

hydrocarbons

TPR MCAT Biochemistry (2 decks)

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